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<h1>Theoretical lipid generation</h1>
<p>Commonly identified lipids within the LipidomicNet consortium are mainly members of the glycerophospholipid category, these lipids all share a similar structure.

The following lipid main classes will represent the base set of main classes from which theoretical lipids will be generated:</p>
<ul>

	<li>Glycerophosphoethanolamine
	<li>Glycerophosphocholine
	<li>Glycerophosphoserine
	<li>Glycerophosphoinositol
	<li>Glycerophosphates
	<li>Glycerophosphoglycerol
</ul>

<p>Of these main classes the following sub class types will be generated:</p>

<ul>
	<li>diacyl
	<li>dialky
	<li>monacy,monoalkyl
<ul>

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    <img src="resources/images/lipid_structure.png" alt="Generic glycerophospholipid structure" title="Generic glycerophospholipid structure"  style="margin: 20px; width:600px">
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<p>This category of lipids is composed of a few parts; headgroup, phosphate, glycerol, linkages and fatty acids. By doing a Cartesian cross of all main classes and linkages we get 18 lipid sub classes that will be the inputs for lipid enumeration. Within a lipid sub class it is the fatty acid composition of lipids that makes them different. Each of these subclasses has two fatty acid R groups, each of which can be anything from a pool of theoretical fatty acids. In order to estimate the chemical bounds for fatty acid generation a survey was conducted amongst LipidomicNet partners and additional lipid scientists at the Babraham Institute. A provisional set of parameters was agreed upon as</p>:
<ul>

	<li>Minimum number of carbons - 2
	<li>Minimum number of carbons - 30
	<li>Odd number of carbon fatty acids - Fatty acid chains may have an odd number of carbons
	<li>Minimum number of double bonds - 0
	<li>Maximum number of double bonds -10
	<li>double bond spacing - Must be spaced at least 2 carbons apart (i.e. conjugated double bonds not allowed).	
</ul>

<p>While these parameters do not reflect the enormous variety of fatty acids synthesised in nature e.g. branch-chain fatty acids. They do reflect a simple test case to prove the methodology upon and will be used to construct a large proportion of the lipids of interest within the LipidomicNet consortium. From this pool of fatty acids a Cartesian cross is performed between fatty acids and sub classes to produce all viable lipids within the defined chemical space</p>


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    <img src="resources/images/lipid_construction.png" alt="Glycerophospholipid construction" title="Glycerophospholipid construction" height="450px" style="margin: 20px;">
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<p>Lipids are created directly as chemical objects using the Chemical Development Kit (CDK)\cite{Steinbeck}. This Java library allows the efficient creation and manipulation of <i>in silico</i> chemicals, with convenience functions to extract properties such as mass, formula and SMILES. The library that performs the theoretical lipid generation is primarily the code of Pablo Moreno who created a stand-alone Java library with all the basic functionality to generate lipid molecule objects given the previously described fatty acid generation parameters and the sub class head group + phosphate + glycerol structures as MOL format files.</p>

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